Merge branch 'main' into fixF3Shortcut

.github/workflows/check-links.yml

@@ -32,7 +32,7 @@ jobs:
           restore-keys: cache-lychee-
       - name: Link Checker
         id: lychee
-        uses: lycheeverse/lychee-action@v2.1.0
+        uses: lycheeverse/lychee-action@v2.2.0
         with:
           fail: true
           args: --accept '200,201,202,203,204,403,429,500' --max-concurrency 1 --cache --no-progress --exclude-all-private './**/*.md'

.github/workflows/deployment-arm64.yml

@@ -69,12 +69,12 @@ jobs:
           submodules: 'true'
           show-progress: 'false'
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].1
+        uses: gittools/actions/gitversion/[email protected].3
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].1
+        uses: gittools/actions/gitversion/[email protected].3
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:

.github/workflows/deployment-jdk-ea.yml

@@ -85,12 +85,12 @@ jobs:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].1
+        uses: gittools/actions/gitversion/[email protected].3
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].1
+        uses: gittools/actions/gitversion/[email protected].3
 
       # JDK
       - name: 'Set up JDK ${{ matrix.jdk }}'

.github/workflows/deployment.yml

@@ -81,12 +81,12 @@ jobs:
           packages: pigz
           version: 1.0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].1
+        uses: gittools/actions/gitversion/[email protected].3
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].1
+        uses: gittools/actions/gitversion/[email protected].3
       - name: Setup JDK
         uses: actions/setup-java@v4
         with:

.github/workflows/tests.yml

@@ -109,7 +109,7 @@ jobs:
           submodules: 'false'
           show-progress: 'false'
       - name: markdownlint-cli2-action
-        uses: DavidAnson/markdownlint-cli2-action@v18
+        uses: DavidAnson/markdownlint-cli2-action@v19
         with:
           globs: |
             *.md

.vscode/settings.json

@@ -2,5 +2,5 @@
     "java.configuration.updateBuildConfiguration": "interactive",
     "java.format.settings.url": "/config/VSCode Code Style.xml",
     "java.checkstyle.configuration": "${workspaceFolder}/config/checkstyle/checkstyle_reviewdog.xml",
-    "java.checkstyle.version": "10.3.4"
+    "java.checkstyle.version": "10.21.0"
 }

CHANGELOG.md

@@ -21,6 +21,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where a bib file with UFF-8 charset was wrongly loaded with a different charset [forum#5369](https://discourse.jabref.org/t/jabref-5-15-opens-bib-files-with-shift-jis-encoding-instead-of-utf-8/5369/)
 - We fixed an issue where new entries were inserted in the middle of the table instead of at the end. [#12371](https://github.com/JabRef/jabref/pull/12371)
 - We fixed an issue where removing the sort from the table did not restore the original order. [#12371](https://github.com/JabRef/jabref/pull/12371)
+- We fixed an issue where JabRef icon merges with dark background [#7771](https://github.com/JabRef/jabref/issues/7771)
+- We fixed an issue where an entry's group was no longer highlighted on selection [#12413](https://github.com/JabRef/jabref/issues/12413)
 
 ### Removed
 

build.gradle

@@ -186,7 +186,7 @@ dependencies {
     implementation 'com.h2database:h2-mvstore:2.3.232'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
-    implementation 'org.bouncycastle:bcprov-jdk18on:1.79'
+    implementation 'org.bouncycastle:bcprov-jdk18on:1.80'
 
     implementation 'commons-cli:commons-cli:1.9.0'
 
@@ -301,7 +301,7 @@ dependencies {
     implementation 'com.vladsch.flexmark:flexmark:0.64.8'
     implementation 'com.vladsch.flexmark:flexmark-html2md-converter:0.64.8'
 
-    implementation group: 'net.harawata', name: 'appdirs', version: '1.2.2'
+    implementation group: 'net.harawata', name: 'appdirs', version: '1.3.0'
 
     implementation group: 'org.jooq', name: 'jool', version: '0.9.15'
     // JAX-RS implemented by Jersey
@@ -310,7 +310,7 @@ dependencies {
     // Implementation of the API
     implementation 'org.glassfish.jersey.core:jersey-server:3.1.10'
     // injection framework
-    implementation 'org.glassfish.jersey.inject:jersey-hk2:3.1.9'
+    implementation 'org.glassfish.jersey.inject:jersey-hk2:3.1.10'
     implementation 'org.glassfish.hk2:hk2-api:3.1.1'
     // testImplementation 'org.glassfish.hk2:hk2-testing:3.0.4'
     // implementation 'org.glassfish.hk2:hk2-testing-jersey:3.0.4'
@@ -391,7 +391,7 @@ dependencies {
     testImplementation "org.testfx:testfx-core:4.0.16-alpha"
     testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
     testImplementation "org.hamcrest:hamcrest-library:3.0"
-    testImplementation "com.github.javaparser:javaparser-symbol-solver-core:3.26.2"
+    testImplementation "com.github.javaparser:javaparser-symbol-solver-core:3.26.3"
 
     // recommended by https://github.com/wiremock/wiremock/issues/2149#issuecomment-1835775954
     testImplementation 'org.wiremock:wiremock-standalone:3.10.0'
@@ -875,7 +875,7 @@ jlink {
 
         if (OperatingSystem.current().isLinux()) {
             imageOptions = [
-                    '--icon', "${projectDir}/src/main/resources/icons/JabRef-icon-64.png",
+                    '--icon', "${projectDir}/src/main/resources/icons/JabRef-linux-icon-64.png",
                     '--app-version', "${project.version}",
             ]
             installerOptions = [

docs/code-howtos/journal-abbreviations.md

@@ -0,0 +1,27 @@
+# Journal Abbreviations
+
+## Preparation
+
+- Ensure that `buildres/abbrv.jabref.org` contains data. Otherwise, the submodules were not configured correctly.
+- Ensure that `build/resources/main/journals/journal-list.mv` exists. It is generated by gradle task `generateJournalListMV`, which uses `org.jabref.cli.JournalListMvGenerator`.
+
+## Where does the data come from?
+
+The generator uses all `.csv` files from <https://github.com/JabRef/abbrv.jabref.org/tree/main/journals>, but ignores following ones:
+
+```java
+        Set<String> ignoredNames = Set.of(
+                // remove all lists without dot in them:
+                // we use abbreviation lists containing dots in them only (to be consistent)
+                "journal_abbreviations_entrez.csv",
+                "journal_abbreviations_medicus.csv",
+                "journal_abbreviations_webofscience-dotless.csv",
+
+                // we currently do not have good support for BibTeX strings
+                "journal_abbreviations_ieee_strings.csv"
+        );
+```
+
+## Future work
+
+See <https://github.com/JabRef/jabref-issue-melting-pot/issues/41>

docs/decisions/0043-show-merge-dialog-when-importing-a-single-pdf.md

@@ -0,0 +1,64 @@
+---
+nav_order: 43
+parent: Decision Records
+---
+# Show merge dialog when importing a single PDF
+
+## Context and Problem Statement
+
+PDF files are one of the main format for transferring various documents, especially scientific papers. However, by itself,
+PDF is like a picture, it contains commands solely for displaying the human-readable text, but it might not contain
+computer-readable metadata.
+
+To overcome these problems various heuristics and AI models are used to "convert" a PDF into a BibTeX entry. However, it
+also introduces a level of problems, as heuristics are not ideal: sometimes it works perfectly, but on others it generates
+random output.
+
+PDF importing in JabRef is done via `PdfImporter` abstract class and its descendants, and via `PdfMergeMetadataImporter`.
+`PdfImporter` is typically a single heuristics or method of extracting a `BibEntry` from PDF. `PdfMergeMetadataImporter`
+collects `BibEntry` candidates from all `PdfImporter`s and merges them automatically into a single `BibEntry`.
+
+The specific problem JabRef has: should JabRef automate all heuristics (automatically merge all `BibEntry`ies from
+several `PdfImporter`s) when importing PDF files or should every file be analysed thoroughly by users?
+
+## Decision Drivers
+
+* Option should provide a good-enough quality.
+* It is desired to have a fine-grained controls of PDF importing for power-users.
+
+## Considered Options
+
+* Automatically merge all `BibEntry` candidates from `PdfImporters`.
+* Open a merge dialog with all candidates.
+* Open a merge dialog with all candidates if a single PDF is imported.
+
+## Decision Outcome
+
+Chosen option: "Open a merge dialog with all candidates if a single PDF is imported", because comes out best (see below).
+
+## Pros and Cons of the Options
+
+### Automatically merge all `BibEntry` candidates from `PdfImporters`
+
+* Good, because minimal user interaction and disruption of flow. It also allows batch-processing.
+* Bad, because heuristics are not ideal, and it is even harder to develop a "smarter" merging algorithm.
+
+### Open a merge dialog with all candidates
+
+* Good, because allows for fine-grained import. Some correct field may be overridden by a wrong field from other importer,
+  which is undesirable for power-users.
+* Bad, because it is a dialog. If lots of PDFs are imported, then there will be lots of dialogs, which might be
+  too daunting to process manually.
+
+### Open a merge dialog with all candidates if a single PDF is imported
+
+Explanation:
+
+- If a single PDF is imported, then open a merge dialog.
+- If several PDFs are imported, merge candidates for each PDF automatically.
+
+Outcomes:
+
+* Good, because it combines the best of the other two options: Allow both for PDF batch-processing and for fine-grained control.
+
+<!-- markdownlint-disable-file MD004 -->

docs/decisions/adr-template.md

@@ -16,7 +16,8 @@ parent: Decision Records
 # consulted: {list everyone whose opinions are sought (typically subject-matter experts); and with whom there is a two-way communication}
 # informed: {list everyone who is kept up-to-date on progress; and with whom there is a one-way communication}
 ---
-<!-- we need to disable MD025, because we use the different heading "ADR Template" in the homepage (see above) than it is foreseen in the template -->
+<!-- We need to disable MD025, because we use the different heading "ADR Template" in the homepage (see above) than it is foreseen in the template. -->
+<!-- Remove these three lines when creating a real ADR - and keep the title consistent. -->
 <!-- markdownlint-disable-next-line MD025 -->
 # {short title, representative of solved problem and found solution}
 

docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-13-code-style.md

@@ -96,7 +96,7 @@ Activate the CheckStyle configuration file by ticking it in the list
 ![JabRef's checkstyle config is activated](guidelines-intellij-checkstyle-jabref-active.png)
 {% endfigure %}
 
-Ensure that the [latest CheckStyle version](https://checkstyle.org/releasenotes.html) is selected (10.3.4 or higher).
+Ensure that the [latest CheckStyle version](https://checkstyle.org/releasenotes.html) is selected (10.21.0 or higher).
 Also, set the "Scan Scope" to "Only Java sources (including tests)".
 
 {% figure caption:"Checkstyle is the highest version - and tests are also scanned" %}

gradle/wrapper/gradle-wrapper.properties

@@ -1,7 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionSha256Sum=7a00d51fb93147819aab76024feece20b6b84e420694101f276be952e08bef03
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.12-bin.zip
+distributionSha256Sum=8d97a97984f6cbd2b85fe4c60a743440a347544bf18818048e611f5288d46c94
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.12.1-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

src/main/java/org/jabref/gui/Base.css

@@ -664,13 +664,7 @@ TextFlow > .tooltip-text-monospaced {
     -fx-padding: 0 0 0 0;
 }
 
-.numberColumn > .hits:any-selected {
-    -fx-background-color: derive(-jr-green, 70%);
-}
 
-.numberColumn > .hits:all-selected {
-    -fx-background-color: -jr-green;
-}
 
 .table-view,
 .tree-table-view {
@@ -2037,6 +2031,14 @@ We want to have a look that matches our icons in the tool-bar */
     -fx-fill: -jr-group-hits-fg;
 }
 
+#groupTree .numberColumn > .hits:any-selected {
+    -fx-background-color: derive(-jr-green, 70%);
+}
+
+#groupTree .numberColumn > .hits:all-selected {
+    -fx-background-color: -jr-green;
+}
+
 #groupTree .expansionNodeColumn {
     -fx-alignment: top-right;
 }

src/main/java/org/jabref/gui/Dark.css

@@ -153,11 +153,11 @@
     -fx-background-color: -fx-light-text-color, -fx-control-inner-background;
 }
 
-.numberColumn > .hits:any-selected {
+#groupTree .numberColumn > .hits:any-selected {
     -fx-background-color: derive(-jr-gray-3, 25%);
 }
 
-.numberColumn > .hits:all-selected {
+#groupTree .numberColumn > .hits:all-selected {
     -fx-background-color: -jr-gray-3;
 }
 

src/main/java/org/jabref/gui/externalfiles/ImportHandler.java

@@ -20,6 +20,7 @@
 import org.jabref.gui.duplicationFinder.DuplicateResolverDialog;
 import org.jabref.gui.fieldeditors.LinkedFileViewModel;
 import org.jabref.gui.libraryproperties.constants.ConstantsItemModel;
+import org.jabref.gui.mergeentries.MultiMergeEntriesView;
 import org.jabref.gui.preferences.GuiPreferences;
 import org.jabref.gui.undo.UndoableInsertEntries;
 import org.jabref.gui.util.DragDrop;
@@ -100,6 +101,7 @@ public ExternalFilesEntryLinker getFileLinker() {
     }
 
     public BackgroundTask<List<ImportFilesResultItemViewModel>> importFilesInBackground(final List<Path> files, final BibDatabaseContext bibDatabaseContext, final FilePreferences filePreferences, TransferMode transferMode) {
+        // TODO: Make a utility class out of this. Package: org.jabref.logic.externalfiles.
         return new BackgroundTask<>() {
             private int counter;
             private final List<ImportFilesResultItemViewModel> results = new ArrayList<>();
@@ -128,11 +130,21 @@ public List<ImportFilesResultItemViewModel> call() {
 
                     try {
                         if (FileUtil.isPDFFile(file)) {
-                            ParserResult pdfImporterResult = contentImporter.importPDFContent(file, bibDatabaseContext, filePreferences);
-                            List<BibEntry> pdfEntriesInFile = pdfImporterResult.getDatabase().getEntries();
-
-                            if (pdfImporterResult.hasWarnings()) {
-                                addResultToList(file, false, Localization.lang("Error reading PDF content: %0", pdfImporterResult.getErrorMessage()));
+                            final List<BibEntry> pdfEntriesInFile;
+
+                            // Details: See ADR-0043
+                            if (files.size() == 1) {
+                                pdfEntriesInFile = new ArrayList<>(1);
+                                UiTaskExecutor.runAndWaitInJavaFXThread(() -> {
+                                    MultiMergeEntriesView dialog = PdfMergeDialog.createMergeDialog(new BibEntry(), file, preferences, taskExecutor);
+                                    dialogService.showCustomDialogAndWait(dialog).ifPresent(pdfEntriesInFile::add);
+                                });
+                            } else {
+                                ParserResult pdfImporterResult = contentImporter.importPDFContent(file, bibDatabaseContext, filePreferences);
+                                pdfEntriesInFile = pdfImporterResult.getDatabase().getEntries();
+                                if (pdfImporterResult.hasWarnings()) {
+                                    addResultToList(file, false, Localization.lang("Error reading PDF content: %0", pdfImporterResult.getErrorMessage()));
+                                }
                             }
 
                             if (pdfEntriesInFile.isEmpty()) {